MRC Transition Support CSF Nicholas Matheson

Lead Research Organisation: University of Cambridge
Department Name: Medicine

Abstract

Approximately 100 years since it was first transmitted to humans, the Human Immunodeficiency Virus (HIV) infects almost 40 million people worldwide, and causes around 1 million AIDS-related deaths every year. It is therefore critical to understand how HIV has been able to replicate and spread, and why HIV infection causes AIDS. "Proteomics" is the large-scale study of "proteins", the critical building blocks of living cells and organisms. I previously used proteomics to measure changes in the number and quantity of proteins at the surface of cells infected with HIV, and identified many proteins specifically depleted by the virus.

Proteins are themselves made up of long chains of "amino acids", and many of the proteins I found to be depleted by HIV are involved in transporting amino acids into cells. These "amino acid transporters" are relatively understudied, and may be attractive candidates for new drugs. I therefore wish to understand why amino acid transporters are targeted by HIV, and the importance of these transporters for "helper T cells", the main cells of the immune system infected by HIV and progressively destroyed in patients with AIDS.

Amongst the HIV targets I identified were proteins called SNAT1 and SERINC3/5. I discovered that SNAT1 transports an amino acid called alanine into cells, and that an abundant supply of alanine is essential for normal helper T cell function. Likewise, SERINC proteins are thought to incorporate an amino acid called serine into "cell membranes", which surround cells and separate their interiors into compartments.

During the first 2.5 years of my Clinician Scientist Fellowship, I have: developed a new way of purifying HIV-infected helper T cells; perfected a way to extract amino acids and other "metabolites" from these cells; and developed a transformative approach to measuring transport of amino acids in and out of cells. I therefore now wish to use these techniques to figure out which metabolic processes in cells are manipulated by HIV, and why they are important for the HIV virus and helper T cells.

In particular, they will enable me to: measure amino acid transport by SNAT1 and SERINC3/5 in growing cells; map global changes in metabolites and metabolism in HIV-infected primary CD4+ T cells; and characterise other critical amino acid transporters of helper T cells identified using different, unrelated approaches earlier in my fellowship. Taken together, these data will be a valuable resource for other researchers in the field and will, I hope, ultimately lead to the development of new treatments for patients targeting amino acid transporters in T cells.

Technical Summary

Approximately 100 years since its transmission to humans, HIV-1 infects almost 40 million people worldwide, and causes around 1 million AIDS-related deaths every year. I previously used TMT-based plasma membrane proteomics to gain a comprehensive, unbiased overview of cell surface proteins regulated by HIV infection. In addition to known targets, I discovered HIV-mediated downregulation of the amino acid transporter SNAT1, and the putative serine carriers SERINC3/5.

I found SNAT1 to be dramatically upregulated at the surface of activated T cells, identified alanine as an endogenous SNAT1 substrate, and showed that extracellular alanine is essential for T cell mitogenesis. Along with SNAT1 and SERINC3/5, I also observed regulation of other transmembrane transporters, suggesting a general paradigm for HIV-mediated manipulation of nutrient uptake and cellular metabolism.

During the first 2.5 years of my Clinician Scientist Fellowship, I have: developed a reporter virus (HIV-AFMACS) allowing magnetic selection of HIV-infected primary CD4+ T cells; optimised a novel method for metabolite extraction from these cells; and developed a transformative stable isotope-based approach to quantitate amino acid transport.

I therefore now wish to leverage these techniques to further elucidate the metabolic processes manipulated by HIV, and define their importance in HIV pathogenesis and T cell immunobiology. In particular, they will enable me to: quantitate amino acid transport by SNAT1 and SERINC3/5 under normal growth conditions in a comprehensive, unbiased fashion; map global metabolic changes in HIV-infected primary CD4+ T cells; and characterise other critical mitogenic amino acid transporters of CD4+ T cells identified by a combined proteomic-genetic screening approach.

Planned Impact

The primary beneficiaries from my results will be other researchers in the fields of retrovirology, immunology and metabolism. I will generate a significant quantity of data that may be shared for added benefit, and will provide a useful resource for the community. To my knowledge, this body of work will represent the first systematic application of stable isotope-based tracing to quantitate amino acid transport. As such, it has the potential to transform the way scientists measure and understand transport of amino acids and other metabolites.

Critically, the novel techniques to quantitate metabolism described in this application are applicable to a wide range of cell biological questions, not just HIV/immunometabolism. I am committed to sharing detailed methods with other researchers, to enhance the efficiency and reproducibility of research in the field. Materials used during this project will also be useful to the wider community, such as the HIV-AFMACS virus. Judging by the number of requests I have previously received for AFMACS reagents, I anticipate that these molecular clones will be in high demand.

Although my proposal involves basic science rather than clinically directed research, it is focused on areas of particular relevance to human disease, with the ultimate aim to deliver novel therapeutic approaches to the clinic. Metabolic pathways targeted by HIV represent candidate targets for antiviral therapy, particularly if they are essential for viral replication but not cellular survival. More immediately, cell surface transporters are readily druggable targets, and cell type specific expression offers the opportunity for focussed immunomodulatory therapies targeting mitogenic pathways such as mTOR in CD4+ T cells.

In a wider context, my time in Matthew's Vander Heiden's laboratory at MIT has provided me with a world-class training in the study of metabolism. I am now using this as a springboard to further develop my research programme in Cambridge, including contributing to the new Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID) Immunometabolic Core facility. There is a growing interest in metabolism within the Department of Medicine and on the campus, and I anticipate that further collaborative and inter-disciplinary projects will be readily forthcoming, with beneficial cross-fertilisation of the research of other groups. I will therefore disseminate my research skills as well as data, and the first beneficiary of this will be my RA.

Publications

10 25 50
 
Description Membership of NIHR Cambridge BioResource Scientific Advisory Board Membership
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Participation in a guidance/advisory committee
URL https://bioresource.nihr.ac.uk/centres-programmes/bioresource-centre-cambridge/
 
Description Engineered SARS-CoV-2 for rapid live virus neutralising antibody assays
Amount £36,255 (GBP)
Funding ID PATH 01 
Organisation NHS Blood and Transplant (NHSBT) 
Sector Public
Country United Kingdom
Start 09/2023 
End 03/2025
 
Description Institutional Strategic Support Fund - Regulation of T cell amino acid tranpsort by the tumour microenvironment
Amount £56,267 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2021 
End 03/2023
 
Description Multiscale analysis of HIV-1-induced small T cell syncytia
Amount $2,703,932 (USD)
Funding ID R01AI172486 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 07/2023 
End 07/2028
 
Description Reserach Grant - Cell-based assays for COVID-19 therapeutics
Amount £17,188 (GBP)
Funding ID #900239 
Organisation Addenbrooke's Charitable Trust (ACT) 
Sector Charity/Non Profit
Country United Kingdom
Start 06/2021 
End 06/2022
 
Description Reserach Grant - INTEGRA ASSIST PLUS pipetting robot for high-throughput assays of neutralising antibodies against SARS-CoV-2
Amount £18,870 (GBP)
Funding ID 900342 
Organisation Addenbrooke's Charitable Trust (ACT) 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2022 
End 03/2023
 
Description SARS COV2 vaccine ResPonse In Obesity - SCORPIO study
Amount £752,294 (GBP)
Funding ID MR/W020564/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 07/2021 
End 08/2023
 
Description Small Research Grant - Protection against SARS-CoV-2 infection by neutralising antibodies (a nested case-control study)
Amount £43,628 (GBP)
Funding ID 119PATH23 
Organisation NHS Blood and Transplant (NHSBT) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2024
 
Description Small Reserach Project Grant - Regulation of HIV replication by virion-associated RNA helicases
Amount £20,000 (GBP)
Organisation British Infection Association (BIA) 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2021 
End 06/2023
 
Description The role of SARS-CoV-2 Nucleocapsid mutations in COVID-19 disease
Amount £38,976 (GBP)
Funding ID REI/1/4943 
Organisation King Abdullah University of Science and Technology (KAUST) 
Sector Academic/University
Country Saudi Arabia
Start 08/2023 
End 08/2024
 
Description The use of convalescent plasma to treat hospitalised and critically ill patients with COVID-19 disease
Amount £3,127,919 (GBP)
Funding ID COVID-19-RECPLAS 
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 04/2020 
End 04/2023
 
Description Transition Support
Amount £209,686 (GBP)
Funding ID MR/T032413/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2021 
End 09/2022
 
Title Luminescent reporter cell line for authentic SARS-CoV-2 infection 
Description During the pandemic, I have applied my knowledge and skills in molecular virology to understanding and combating COVID-19. In particular, my lab has developed luminescent 'reporter cells', which emit light when they are infected with SARS-CoV-2. These allow us to test antiviral drugs, and measure 'neutralising antibodies' in blood samples from patients. We have made them available to the research community via the National Institute for Biological Standards and Control (NIBSC), catalogue number 101062, and the National Institute of Allergy and Infectious Diseases (NIAID)/BEI Resources, catalog no. NR-58714. This work has contributed to >10 collaborative research projects within the Department of Medicine, with other groups at the University of Cambridge, and with external collaborators. Across these collaborations, we have already tested >1,500 samples (contributing so far to 8 published manuscripts, 3 manuscripts in revision or under review, and several presentations at national conferences). The continuing evolution and spread of new SARS-CoV-2 variants of concern, with increasing ability to evade the humoral immune response, has highlighted how important it is to have the capability to measure variant-specific neutralising antibodies against authentic viral isolates (such as Omicron BA.1). 
Type Of Material Cell line 
Year Produced 2021 
Provided To Others? Yes  
Impact Brevini T, Maes M, Webb GJ, Fuchs CD, Buescher G, , Matheson NJ, et al. FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2. Nature. 2022. doi.org/10.1038/s41586-022-05594-0. PMID: 36470304 Touizer E, Alrubayyi A, , Matheson NJ, Morris E, Peppa D, McCoy LE. Attenuated humoral responses in HIV after SARS-CoV-2 vaccination linked to B cell defects and altered immune profiles. iScience. 2023;26(1):105862. doi: 10.1016/j.isci.2022.105862. PMID: 36590902 Shilts J, Crozier TWM, Teixeira-Silva A, , Matheson NJ, Lehner PJ, Wright GJ. LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein. PLoS Biol. 2023;21(2):e3001959. doi: 10.1371/journal.pbio.3001959. PMID: 36735681 Pereyra Gerber P, Donde MJ, Matheson NJ, Taylor A. XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection. Nat Commun. 2022;13(1):6716. PMID: 36385143 Pereyra Gerber P, Duncan LM, Greenwood EJD, Marelli S, Naamati A, , Matheson NJ. A protease-activatable luminescent biosensor and reporter cell line for authentic SARS-CoV-2 infection. PLoS Pathog. 2022;18(2):e1010265. doi: 10.1371/journal.ppat.1010265. PMID: 35143592 Meng B, Abdullahi A, Ferreira IATM, , Matheson NJ, Sato K, Gupta RK. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature. 2022. doi: 10.1038/s41586-022-04474-x. PMID: 35104837 Kotagiri P, Mescia F, Rae W, Bergamaschi L, Tuong Z, , Matheson NJ, et al. B Cell Receptor Repertoire Kinetics after SARS-CoV-2 Infection and Vaccination. Cell Rep. 2022;38(7):110393. doi: 10.1016/j.celrep.2022.110393. PMID: 35143756 Bergamaschi L, Mescia F, Turner L, Hanson AL, Kotagiri P, , Matheson NJ, et al. Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease. Immunity. 2021;54(6):1257-75 e8. Epub 2021/05/30. doi: 10.1016/j.immuni.2021.05.010. PMID: 34051148 
URL https://www.nibsc.org/products/brm_product_catalogue/detail_page.aspx?catid=101062
 
Description Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration 
Organisation National Institute for Health Research
Department NIHR Cambridge Biomedical Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution I am one of the Principal Investigators contributng to the CITIID-NIHR COVID-19 BioResource Collaboration, led by Professor Smith (CITIID) and Professory Bradley (NIHR). My lab has been particularly responsible for measuring neutralising antibody levels against SARS-CoV-2 in blood samples from patients
Collaborator Contribution As part of the NIHR BioResource, this collaborative project has allowed people tested in hospital for COVID-19 to participate in research by providing biological samples (such as blood, and the swab used to test for COVID-19) and answering some questions about their lifestyle and mental health. NHS staff undergoing routine screening for COVID-19 have also been asked if they would like to participate, in order to safely collect samples representing a variety of COVID-19 experiences - from those displaying none or mild symptoms to those with more severe experiences. The samples have been used to support current and future research - including on-going research to find new and faster ways to test patients and staff, understand why the virus affects people in different ways and find new ways to treat the disease
Impact 30 publications so far indexed on PubMed (PMIDs): 36721385, 36717723, 36451358, 36420270, 36343994, 36330526, 36065116, 36058413, 35963244, 35864233, 35864232, 35224470, 35189575, 35143756, 35104837, 34488225, 34260717, 34192737, 34051148, 33879890, 33706364, 33619509, 33545711, 33398302, 33318491, 32905045, 32838340, 32737467, 32558644, 32392129
Start Year 2020
 
Description Collaboration with Thali laboratory 
Organisation University of Vermont
Country United States 
Sector Academic/University 
PI Contribution I have created a functional proteomic atlas of HIV infection in primary human CD4+ T-cells, in which we identified over 650 specific HIV-dependent changes, including almost 200 proteins not previously identified or known to be regulated in T cell lines
Collaborator Contribution Professor Thali has made key contributions to study of HIV, including the development of a novel technique allowing the magnetic selection of HIV-induced T cell syncytia. We continue to collaborate on the proteomic analysis of these syncytia
Impact Whitaker EE, Matheson NJ, Perlee S, Munson PB, Symeonides M, Thali M. EWI-2 Inhibits Cell-Cell Fusion at the HIV-1 Virological Presynapse. Viruses. 2019;11(12). Epub 2019/11/24. doi: 10.3390/v11121082. PMID: 31757023
Start Year 2019
 
Description Collaboration with Vander Heiden laboratory 
Organisation Massachusetts Institute of Technology
Department Koch Institute
Country United States 
Sector Academic/University 
PI Contribution I was a Visiting Scientist in the Vander Heiden laboratory at the David H Koch Institute for Integrative Cancer Research (MIT) 2017-18. I learnt to apply stable isotope-based metabolite tracing and metabolic flux analysis in an interdisciplinary project aimed at understanding metabolism in HIV-infected cells. I have subsequently used these skills to set up a GCMS-based metabolomic pipeline at the University of Cambridge. We continue to collaborate on projects related to immunometabolism
Collaborator Contribution Professor Vander Heiden has made key contributions in the field of cancer metabolism, and is co-sponsor of my MRC Clinician Scientist Fellowship. His laboratory provided training on stable isotope-based metabolite tracing and metabolic flux analysis. We continue to collaborate on projects related to immunometabolism
Impact Luengo A, Li Z, Gui DY, Sullivan LB, Zagorulya M, Do BT, Ferreira R... Matheson NJ, Vander Heiden MG. (2020). Increased demand for NAD relative to ATP drives aerobic glycolysis. Mol Cell. 2021 Feb 18;81(4):691-707.e6. doi: 10.1016/j.molcel.2020.12.012 Lau AN, Li Z, Danai LV, Westermark AM, Darnell AM, Ferreira R, Gocheva V... Matheson NJ, Yilmaz O, Vander Heiden MG. (2020). Dissecting cell-type-specific metabolism in pancreatic ductal adenocarcinoma. eLife. 2020 Jul 10;9:e56782. doi: 10.7554/eLife.56782
Start Year 2017